Protein tyrosine kinase inhibitors

Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds

Intuitive, visual rendering--mapping--of high-dimensional chemical spaces (CS), is an important topic in chemoinformatics. Such maps were so far dedicated to specific compound collections--either limited series of known activities, or large, even exhaustive enumerations of molecules, but without associated property data. Typically, they were challenged to answer some classification problem with respect to those same molecules, admired for their aesthetical virtues and then forgotten--because they were set-specific constructs. This work wishes to address the question whether a general, compound set-independent map can be generated, and the claim of "universality" quantitatively justified, with respect to all the structure-activity information available so far--or, more realistically, an exploitable but significant fraction thereof. The "universal" CS map is expected to project molecules from the initial CS into a lower-dimensional space that is neighborhood behavior-compliant with respect to a large panel of ligand properties. Such map should be able to discriminate actives from inactives, or even support quantitative neighborhood-based, parameter-free property prediction (regression) models, for a wide panel of targets and target families. It should be polypharmacologically competent, without requiring any target-specific parameter fitting. This work describes an evolutionary growth procedure of such maps, based on generative topographic mapping, followed by the validation of their polypharmacological competence. Validation was achieved with respect to a maximum of exploitable structure-activity information, covering all of Homo sapiens proteins of the ChEMBL database, antiparasitic and antiviral data, etc. Five evolved maps satisfactorily solved hundreds of activity-based ligand classification challenges for targets, and even in vivo properties independent from training data. They also stood chemogenomics-related challenges, as cumulated responsibility vectors obtained by mapping of target-specific ligand collections were shown to represent validated target descriptors, complying with currently accepted target classification in biology. Therefore, they represent, in our opinion, a robust and well documented answer to the key question "What is a good CS map?"

Small-molecule inhibitors of NADPH oxidase 4

NOX enzymes are the major contributors in many oxidative damage related diseases. Unfortunately, at present no specific NOX inhibitor is available. Here, we describe the discovery and development of novel NOX4 inhibitors. Compound libraries were tested in a cell-based assay as a primary screen, monitoring H2O2 production. Twenty-four compounds inhibited Nox4 activity with low-micromolar IC(50) values of which three were selected for further drug development.

QSAR study of p56(lck) protein tyrosine kinase inhibitory activity of flavonoid derivatives using MLR and GA-PLS

Quantitative relationships between molecular structure and p56(lck) protein tyrosine kinase inhibitory activity of 50 flavonoid derivatives are discovered by MLR and GA-PLS methods. Different QSAR models revealed that substituent electronic descriptors (SED) parameters have significant impact on protein tyrosine kinase inhibitory activity of the compounds. Between the two statistical methods employed, GA-PLS gave superior results. The resultant GA-PLS model had a high statistical quality (R(2) = 0.74 and Q(2) = 0.61) for predicting the activity of the inhibitors. The models proposed in the present work are more useful in describing QSAR of flavonoid derivatives as p56(lck) protein tyrosine kinase inhibitors than those provided previously.

Role of a tyrosine kinase in the CO2-induced stimulation of HCO3−reabsorption by rabbit S2 proximal tubules

A previous study demonstrated that proximal tubule cells regulate HCO3−reabsorption by sensing acute changes in basolateral CO2concentration, suggesting that there is some sort of CO2sensor at or near the basolateral membrane (Zhou Y, Zhao J, Bouyer P, and Boron WF Proc Natl Acad Sci USA 102: 3875–3880, 2005). Here, we hypothesized that an early element in the CO2signal-transduction cascade might be either a receptor tyrosine kinase (RTK) or a receptor-associated (or soluble) tyrosine kinase (sTK). In our experiments, we found, first, that basolateral 17.5 μM genistein, a broad-spectrum tyrosine kinase inhibitor, virtually eliminates the CO2sensitivity of HCO3−absorption rate ( J[Formula: see text]). Second, we found that neither basolateral 250 nM nor basolateral 2 μM PP2, a high-affinity inhibitor for the Src family that also inhibits the Bcr-Abl sTK as well as the Kit RTK, reduces the CO2-stimulated increase in J[Formula: see text]. Third, we found that either basolateral 35 nM PD168393, a high-affinity inhibitor of RTKs in the erbB (i.e., EGF receptor) family, or basolateral 10 nM BPIQ-I, which blocks erbB RTKs by competing with ATP, eliminates the CO2sensitivity. In conclusion, the transduction of the CO2signal requires activation of a tyrosine kinase, perhaps an erbB. The possibilities include the following: 1) a TK is simply permissive for the effect of CO2on J[Formula: see text]; 2) a CO2receptor activates an sTK, which would then raise J[Formula: see text]; 3) a CO2receptor transactivates an RTK; and 4) the CO2receptor could itself be an RTK.

Mechanisms of suppression of nitric oxide production by 3-O-methylquercetin in RAW 264.7 cells

Rhamnus nakaharai Hayata (Rhamnaceae) is used as a folk medicine in Taiwan for treating constipation, inflammation, tumors, and asthma. 3-O-Methylquercetin (3-MQ), a main constituent of the plant, has been reported to have potential for use in the treatment of asthma. The mechanisms of anti-inflammation of 3-MQ are still unclear. Nitric oxide (NO) production induced by lipopolysaccharide (LPS) through iNOS expression in RAW 264.7 cells, a mouse macrophage cell line, may reflect the degree of inflammation and may provide a measure for assessing the effect of drugs on the inflammatory process. Therefore, we were interested in investigating the mechanisms of suppression of NO production by 3-MQ in RAW 264.7 cells. 3-MQ (1-10 microM) concentration-dependently inhibited LPS (100 ng/mL)-induced NO production in RAW 264.7 cells. The IC(50) value was calculated to be 4.23 microM. 3-MQ (1-10 microM) significantly and concentration-dependently inhibited LPS (100 ng/mL)-induced iNOS protein and mRNA expressions in cells. The IC(50) values were calculated to be 4.36 and 6.53 microM, respectively. There was no significant difference among these three IC(50) values of 3-MQ. In conclusion, 3-MQ may exert its anti-inflammatory effect through the inhibition of iNOS DNA transcription.

QSAR study of flavonoid derivatives as p56lck tyrosinkinase inhibitors

QSAR studies on 104 flavonoid derivatives as p56lck protein tyrosine kinase inhibitors were performed using hydration energy and logP as predictor parameters. The results obtained demonstrate in detail, which specify that hydration energy and hydrophobic parameters of the compounds play a significant role in developing QSAR models. The significance of presence and absence of substituents on particular position is successfully explored with the help of indicator parameters. The results are critically discussed on the basis of multiple linear regression parameters.

A role for MAP kinase in regulating ectodomain shedding of APLP2 in corneal epithelial cells

We previously reported an increased secretion of amyloid precursor-like protein 2 (APLP2) in the healing corneal epithelium. The present study sought to investigate signal transduction pathways involved in APLP2 shedding in vitro. APLP2 was constitutively shed and released into culture medium in SV40-immortalized human corneal epithelial cells as assessed by Western blotting, flow cytometry, and indirect immunofluorescence. Activation of protein kinase C (PKC) by phorbol 12-myristate 13-acetate (PMA) caused significant increases in APLP2 shedding. This was inhibited by staurosporine and a PKC-epsilon-specific, N-myristoylated peptide inhibitor. Epidermal growth factor (EGF) also induced APLP2 accumulation in culture medium. Basal APLP2 shedding as well as that induced by PMA and EGF was blocked by a mitogen-activated protein kinase (MAPK) kinase inhibitor, U-0126. Our results suggest that MAPK activity accounts for basal as well as PKC- and EGF-induced APLP2 shedding. In addition, PKC-epsilon may be involved in the induction of APLP2 shedding in corneal epithelial cells.

Phosphatidic acid regulates tyrosine phosphorylating activity in human neutrophils: enhancement of Fgr activity

In human neutrophils, the activation of phospholipase D and the Tyr phosphorylation of proteins are early signaling events upon cell stimulation. We found that the pretreatment of neutrophils with ethanol (0.8%) or 1-butanol (0.3%), which results in the accumulation of phosphatidylalcohol at the expense of phosphatidic acid (PA), decreased the phorbol myristate acetate-stimulated Tyr phosphorylation of endogenous proteins (42, 115 kDa). When neutrophil cytosol was incubated in the presence or absence of PA, these and other endogenous proteins became Tyr-phosphorylated in a PA-dependent manner. In contrast, phosphatidylalcohols exhibited only 25% (phosphatidylethanol) or 5% (phosphatidylbutanol) of the ability of PA to stimulate Tyr phosphorylation in the cell-free assay. Similarly, other phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, phosphatidylinositol, polyphosphoinositides, and sphingosine 1-phosphate) showed little ability to stimulate Tyr phosphorylation. These data suggest that PA can function as an intracellular regulator of Tyr phosphorylating activity. Gel filtration chromatography of leukocyte cytosol revealed a peak of PA-dependent Tyr phosphorylating activity distinct from a previously described PA-dependent phosphorylating activity (Waite, K. A., Wallin, R., Qualliotine-Mann, D., and McPhail, L. C. (1997) J. Biol. Chem. 272, 15569-15578). Among the protein Tyr kinases expressed in neutrophils, only Fgr eluted exclusively in the peak of PA-dependent Tyr phosphorylating activity. Importantly, Fgr isolated from unstimulated neutrophil lysates showed increased activity in the presence of PA but not phosphatidylbutanol. Moreover, the pretreatment of neutrophils with 1-butanol decreased Fgr activity in cells stimulated with formyl-methionyl-leucyl phenylalanine plus dihydrocytochalasin B. Together, these results suggest a new second messenger role for PA in the regulation of Tyr phosphorylation.

Roles of tyrosine kinase and protein kinase C in infarct size limitation by repetitive ischemic preconditioning in the rat

In this study, we examined the possibility that infarct-size limitation by repetitive preconditioning (PC) is achieved by activation of both protein kinase C (PKC) and tyrosine kinase. In addition, we assessed whether such kinase activation is triggered by angiotensin II type 1 (AT1) and alpha1-adrenergic receptors and whether sarcolemmal and mitochondrial adenosine triphosphate (ATP)-sensitive potassium (K(ATP)) channels play roles as effectors of cardioprotection in the rat. Under pentobarbital anesthesia, myocardial infarction was induced by 20-min coronary occlusion and 3-h reperfusion in the rat. Infarct size was determined by tetrazolium and expressed as a percentage of area at risk (%IS/AR). PC with one cycle of 5-min ischemia/5-min reperfusion before 20-min ischemia significantly reduced %IS/AR from the control value of 49.4 +/- 2.0 to 35.4 +/- 2.8, and repetitive PC with two cycles of 5-min ischemia/5-min reperfusion further limited %IS/AR to 3.2 +/-0.9. Infarct-size limitation by single-cycle PC was completely abolished by a PKC inhibitor, staurosporine (100 microg/kg; %IS/ AR, 45.7 +/- 5.0). In contrast, the cardioprotection by repetitive PC was only partially blocked by staurosporine (%IS/AR, 19.8 +/- 2.4), another PKC inhibitor, polymyxin B (5 mg/kg; %IS/AR, 16.2 +/- 3.1), or a tyrosine kinase inhibitor, genistein (5 mg/kg; %IS/AR, 21.8 +/- 1.4). However, a combined injection of genistein and staurosporine additively inhibited protection of repetitive PC (%IS/AR, 36.4 +/- 1.7). Staurosporine, polymyxin B, or genistein alone did not modify %IS/AR in nonpreconditioned rat hearts. Infarct-size limitation by repetitive PC was not attenuated by pretreatment with a selective AT1-receptor blocker (CV11974, 10 mg/kg), prazosin (0.6 mg/kg; %IS/AR, 6.4 +/- 3.2 and 1.6 +/- 0.5, respectively). A selective blocker of mitochondrial K(ATP) channels, 5-hydroxydecanoate (3 mg/kg), completely abolished the cardioprotective effect (%IS/AR, 50.8 +/-3.5), but HMR1883 (3 mg/kg), a selective blocker of sarcolemmal K(ATP) channels, failed to inhibit the preconditioning effect (%IS/AR, 4.4 +/- 0.7). These findings suggest that repetition of PC provokes activation of both PKC and tyrosine kinase, leading to enhanced antiinfarct tolerance by opening of mitochondrial but not sarcolemmal K(ATP) channels. It is unlikely that activation of either AT1 or alpha1-adrenergic receptor alone is crucial to trigger preconditioning. Key Words: Tyrosine kinase-Genistein-Angiotensin II-alpha1-Adrenergic receptor-Sarcolemmal K(ATP) channel-Mitochondrial K(ATP) channel.

Parathyroid hormone stimulates extracellular signal-regulated kinase (ERK) activity through two independent signal transduction pathways: role of ERK in sodium-phosphate cotransport

Parathyroid hormone (PTH), a major physiologic regulator of proximal renal tubule cell sodium-phosphate cotransport, stimulates several signal transduction pathways including extracellular signal-regulated kinases (ERK). The physiologic role of PTH-stimulated ERK is unknown. The purpose of the present study was to identify signaling components involved in PTH-stimulated ERK activity and to determine the role of PTH-stimulated ERK activity in regulation of phosphate transport. PTH-stimulated ERK activity was measured in opossum kidney (OK) cell lysates as phosphorylation of myelin basic protein by an in vitro kinase assay. PTH stimulated a dose-dependent increase in ERK activity with a peak at 10(-7) M. The time course was biphasic with an early peak at 10 min and a later peak at 20 min. Pretreatment of OK cells with the nonreceptor tyrosine kinase inhibitors genistein and herbimycin A or with the phosphatidylinositol 3-kinase (PI-3K) inhibitors wortmannin and LY294002 blocked the early and late peaks of PTH-stimulated ERK activity. Pretreatment with the protein kinase C inhibitor calphostin C blocked only the later phase of PTH-stimulated ERK. To determine the role of ERK in regulation of phosphate transport, PTH inhibition of phosphate uptake and PTH regulation of sodium-phosphate cotransporter (NaPi-4) expression were measured in OK cells pretreated with the MEK inhibitor PD098059. PD098059 significantly attenuated PTH inhibition of phosphate uptake but did not prevent PTH downregulation of NaPi-4. It is concluded that PTH stimulates ERK through two signal transduction pathways: an early pathway dependent on tyrosine kinase and PI-3K and a late pathway dependent on protein kinase C. PTH-stimulated ERK regulates phosphate transport by a mechanism other than downregulation of NaPi-4 expression.

IkappaB kinases alpha and beta show a random sequential kinetic mechanism and are inhibited by staurosporine and quercetin

Activation of transcription factor NF-kappaB is regulated by phosphorylation and subsequent degradation of its inhibitory subunit IkappaB. The signal-induced phosphorylation of IkappaB involves two IkappaB kinases, IKKalpha and IKKbeta. In the present study, we investigated the kinetic mechanisms of IKKalpha and IKKbeta by substrate and product inhibition. For both IKKalpha and IKKbeta, the product ADP was a competitive inhibitor versus ATP and a non-competitive inhibitor versus IkappaBalpha. An alternative peptide substrate, IkappaBalpha-(21-41), was a competitive inhibitor versus IkappaBalpha and a non-competitive inhibitor versus ATP for both kinases. These results rigorously eliminate the possibility of an ordered sequential mechanism and demonstrate that both kinases have a random sequential bi bi mechanism. Two natural compounds, quercetin and staurosporine, had previously been shown to inhibit the NF-kappaB pathway, but the molecular target(s) of these compounds in the event had not been established. Here we demonstrate that quercetin and staurosporine potently inhibit both IKKalpha and IKKbeta. Daidzein, a quercetin analogue that does not inhibit NF-kappaB activation, showed no significant inhibition of either enzyme. This suggests that the inhibitory properties of quercetin and staurosporine in the NF-kappaB pathway are mediated in part by their inhibition of IKKalpha and IKKbeta. Mechanism studies reveal that staurosporine is a competitive inhibitor versus ATP, whereas quercetin serves as a mixed type inhibitor versus ATP. The strong inhibition of IKKbeta by staurosporine (K(i) = 172 nM) and ADP (K(i) = 136 nM) provides a rationale and structural framework for designing potent ATP-site inhibitors of IKKbeta, which is an attractive drug target for inflammatory diseases.

Protein tyrosine kinase inhibitors as novel therapeutic agents

Protein tyrosine kinases (PTKs) play a key role in normal cell and tissue development. Enhanced PTK activity is intimately correlated with proliferative diseases, such as cancers, leukemias, psoriasis, and restenosis. This realization prompted us to systematically synthesize tyrosine phosphorylation inhibitors (tyrphostins) as potential drugs. Over the years, we have demonstrated the ability to synthesize selective tyrphostins aimed at different receptor, as well as at nonreceptor, tyrosine kinases. Some of these tyrphostins have shown efficacy in vivo as antileukemic agents and antirestenosis agents. AG 490, a Jak-2 inhibitor, is potent against recurrent pre-B acute lymphoblastic leukemia. AG 1295, a selective platelet-derived growth factor receptor kinase inhibitor, inhibits 50% of balloon injury-induced stenosis in the phemoral arteries of pigs. AG 1517 (SU 5271), a potent epiderminal growth factor receptor kinase inhibitor, is currently in clinical trials for psoriasis. Similarly, SU 5416, a potent kinase inhibitor of the vascular endothelial growth factor receptor/kinase domain receptor/Flk-1, is currently in clinical trials as an anticancer agent by virtue of its strong anti-angiogenic activity. These findings demonstrate that the identification of PTKs that play a key role in a defined disease state can lead to a selective drug. Tyrphostins also show efficacy in vivo in inflammatory diseases such as sepsis, cirrhosis, and experimental autoimmune encephalitis.

Structure-based design of peptidomimetic ligands of the Grb2-SH2 domain

We have designed and synthesized a (3-aminomethyl-phenyl)-urea scaffold to mimic the X+1-Asn part of the minimal phosphopeptide sequence, Ac-pTyr-X+1-Asn-NH2, recognized by the Grb2-SH2 domain. The resulting compounds show the same degree of affinity as their peptide counterparts for the Grb2-SH2 domain. This is the first example reported to date of ligands of the Grb2-SH2 domain with substantially reduced peptidic character.

The development of novel and selective p56lck tyrosine kinase inhibitors

Early T-cell receptor mediated signal transduction involves the activation of several tyrosine protein kinases. One of these tyrosine kinases, p56lck, is expressed primarily in T-cells and Natural Killer (NK) cells and has been shown to be critical for their proliferative and effector functions. Indandiones have been identified as a potent and selective chemical class that inhibits p56lck.

Increased tyrosine phosphorylation and novel cis-acting element mediate activation of the fibroblast growth factor-2 (FGF-2) gene by nicotinic acetylcholine receptor. New mechanism for trans-synaptic regulation of cellular development and plasticity

FGF-2, a mitogenic/neurotrophic protein, controls the development and plasticity of many types of neural cells. In neural crest-derived adrenal pheochromatocytes, induction of FGF-2 coincides with the establishment of functional innervation and is reproduced in vitro by stimulating acetylcholine receptors (AChR). The mechanisms by which AChR activate the FGF-2 gene were examined in cultured bovine adrenal medullary chromaffin (BAMC) cells in which AChR induce expression and nuclear accumulation of growth-promoting FGF-2 and FGF-2 receptors. Carbachol or nicotine increased expression of transfected FGF-2 gene promoter-luciferase constructs and were more potent than the muscarinic agonist ABMCB. Deletion analysis has identified a unique -555/-512 bp element that confers AChR stimulation and basal activity to the downstream FGF-2 promoter, and a separate protein kinase C/cAMP-responsive sequence (-625/-555 bp). Stimulation of AChR increased in vitro formation of protein complexes with the AChR-responsive element which were not displaced by target oligonucleotides for common trans-activators. Southwestern analysis identified 50-55, 125, 140 and 170 kDa proteins that interact with the AChR-responsive element in a manner stimulated by AChR. Nicotine increased tyrosine phosphorylation of cytoplasmic and nuclear proteins, including 50-55 kDa promoter-binding factors. Activation of the FGF-2 promoter was reduced by genistein. Thus, nicotinic AChR activate the FGF-2 gene via a new signaling mechanism separate from the cAMP/PKC pathways. It utilizes tyrosine phosphorylation and interaction of trans-activating factors with a novel cis-acting element. It offers a new pathway through which trans-synaptic signals may control neural development and plasticity.

The design, synthesis and activity of pentapeptide pp60c-src inhibitors containing L-phosphotyrosine mimics

Efficient syntheses of 4-(R,S-hydroxyphosphonomethyl)-L-phenylalanine and 4-carboxy-L-phenylalanine within the context of the pentapeptide Ac-Ile-X-Gly-Glu-Phe-NH2 (wherein X = the unnatural amino acid) illustrate the use of a divergent synthetic strategy from an advanced common peptide intermediate to more readily access peptide-based tyrosine kinase inhibitors. The key intermediate, Ac-Ile-Phe(4-formyl)-Gly-Glu(O-tBu)-Phe-NH2, was synthesized by a facile palladium-catalyzed carbonylation of Ac-Ile-Phe(4-iodo)-Gly-Glu(O-tBu)-Phe-NH2. Oxidation of Ac-Ile-Phe(4-formyl)-Gly-Glu(O-tBu)-Phe-NH2 with tetrabutylammonium permanganate or addition of di-t-butylphosphite, both followed by trifluoroacetic acid deprotection, gave the target pentapeptide inhibitors wherein X = 4-carboxy-L-phenylalanine or 4-(R,S-hydroxyphosphonomethyl)-L-phenylalanine, respectively. These two peptides gave somewhat more potent inhibition of the tyrosine kinase pp60c-src than the corresponding pentapeptide wherein X = L-phenylalanine, demonstrating that appended functionalities at the 4-position are accepted and can enhance binding through added interactions within the catalytic region of the active site.

Design of allele-specific inhibitors to probe protein kinase signaling

BACKGROUND

Deconvoluting protein kinase signaling pathways using conventional genetic and biochemical approaches has been difficult because of the overwhelming number of closely related kinases. If cell-permeable inhibitors of individual kinases could be designed, the role of each kinase could be systematically assessed.

RESULTS

We have devised an approach combining chemistry and genetics to develop the first highly specific cell-permeable inhibitor of the oncogenic tyrosine kinase v-Src. A functionally silent active-site mutation was made in v-Src to distinguish it from all other cellular kinases. A tight-binding cell-permeable inhibitor of this mutant kinase that does not inhibit wild-type kinases was designed and synthesized. In vitro and whole-cell assays established the unique specificity of the mutant v-Src-inhibitor pair. The inhibitor reversed cell transformation by the engineered but not the 'wild type' v-Src, establishing that changes in cellular signaling can be attributed to specific inhibition of the engineered kinase. The generality of the method was tested by engineering another tyrosine kinase, Fyn, to contain the corresponding active-site mutation to the one in v-Src. The same compound that inhibited mutant v-Src could also potently inhibit the engineered Fyn kinase.

CONCLUSIONS

Allele-specific cell-permeable inhibitors of individual Src family kinases can be rapidly developed in an approach that should be applicable to all kinases. This approach will be useful for the deconvolution of kinase-mediated cellular pathways and for validating novel kinases as good targets for drug discovery both in vitro and in vivo.